Development and application of QM/MM methods for metalloenzymes

金属酶QM/MM方法的开发与应用

基本信息

批准号：
8847341
负责人：
Qiang Cui
金额：
$ 24.22万
依托单位：
UNIVERSITY OF WISCONSIN-MADISON
依托单位国家：
美国
项目类别：
财政年份：
2013
资助国家：
美国
起止时间：
2013-09-01 至 2016-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8847341
关键词：
Active Sites Address Alkaline Phosphatase Benchmarking Binding Biological Process Chemistry Complex Computational Technique Computing Methodologies Copper Coupled Cyclic AMP-Dependent Protein Kinases Data Dependence Development Disease Drug Formulations Electron Transport Elements Employee Strikes Enzymes Equilibrium Esters Free Energy Geometry Health Human Hybrids Inorganic Sulfates Ions Isotopes Kinetics Malignant Neoplasms Metalloproteins Metals Methodology Methods Modeling Mono-S Mutation Nature Neurodegenerative Disorders Oxidation-Reduction Performance Play Property Proteins Reaction Research Role Sampling Set protein Site Site-Directed Mutagenesis Solvents Staging System Testing Transition Elements Unspecified or Sulfate Ion Sulfates Zinc base blind combat computer studies cytochrome c oxidase density design experience flexibility improved inorganic phosphate insight interest member metalloenzyme nanosecond next generation novel novel strategies research study simulation small molecule theories tool

项目摘要

DESCRIPTION (provided by applicant): Metalloenzymes are important but challenging targets for computational studies because a reliable and computationally efficient potential function for the metal site is not straightforward to obtain. The challenges are particularly severe for metalloenzymes that feature structurally flexible active sites and/or dynamical metal coordination spheres, for which good examples include metalloenzymes with open active sites and thus promiscuous catalytic activities and proteins whose metal coordination sphere undergoes major redox/pH-coupled changes. Here we propose to develop novel QM/MM methods based on the latest formulation of density functional tight binding (DFTB3) approach to strike the proper balance of computational efficiency and accuracy for metalloenzymes. The specific aims are: 1. Parameterize DFTB3 for closed-shell systems (Mg, Zn, P and S) to facilitate the study of reactivity in flexible metalloenzymes that employ Mg and Zn as co-factors. Refine a novel DFTB3-MM interaction Hamiltonian and a multi-level QM/MM free energy framework that judiciously combines DFTB3/MM and high-level QM/MM potentials. The methods will be carefully benchmarked with both small molecule and metalloenzyme systems. 2. As an application to closed-shell metalloenzymes, dissect the catalytic mechanism of AP superfamily enzymes with both cognate and non-cognate substrates. Test the hypothesis that the remarkable catalytic promiscuity observed for the AP superfamily members is due to the significant structural flexibilities of the bi-metallic active site, which is able to recognize trasition states of distinct nature for different substrates. Test the computational results by comparing relevant observables (linear free energy relations, kinetic isotope effects, mutation and thio-effects) to experiments. 3. Introduce orbital angular momentum dependence of the Hubbard parameters into spin-polarized DFTB approach for the description of open-shell species. We will focus on the parameterization for copper and the method will be systematically tested and refined by comparing structural and energetic (e.g., reduction potential and pKa) properties of small molecules and copper proteins. Apply the approach to resolve several outstanding questions regarding the pH dependence of redox properties in blue copper proteins, setting the stage for applications to more complex problems, such as the binding of copper to proteins implicated in neurodegenerative diseases.

描述（由申请人提供）：金属酶对于计算研究来说是重要但具有挑战性的目标，因为金属位点的可靠且计算高效的势函数并不容易获得。对于具有结构灵活的活性位点和/或动态金属配位球的金属酶来说，挑战尤其严峻，其中很好的例子包括具有开放活性位点并因此具有混杂催化活性的金属酶以及其金属配位球经历主要氧化还原/pH耦合变化的蛋白质。在这里，我们建议开发基于密度功能紧结合 (DFTB3) 方法最新公式的新型 QM/MM 方法，以在金属酶的计算效率和准确性之间取得适当的平衡。具体目标是： 1. 参数化闭壳体系（Mg、Zn、P 和 S）的 DFTB3，以促进以 Mg 和 Zn 作为辅助因子的柔性金属酶的反应性研究。完善新颖的 DFTB3-MM 相互作用哈密顿量和多级 QM/MM 自由能框架，明智地将 DFTB3/MM 和高级 QM/MM 势结合起来。这些方法将与小分子和金属酶系统进行仔细的基准测试。 2. 作为闭壳金属酶的应用，剖析具有同源和非同源底物的 AP 超家族酶的催化机制。测试以下假设：AP 超家族成员观察到的显着催化混杂性是由于双金属活性位点的显着结构灵活性所致，该双金属活性位点能够识别不同底物的不同性质的转变状态。通过将相关可观测值（线性自由能关系、动力学同位素效应、突变和硫效应）与实验进行比较来测试计算结果。 3. 将哈伯德参数的轨道角动量依赖性引入自旋极化 DFTB 方法中以描述开壳层物质。我们将重点关注铜的参数化，并通过比较小分子和铜蛋白的结构和能量（例如还原电位和 pKa）特性来系统地测试和完善该方法。应用该方法解决了有关蓝铜蛋白氧化还原特性的 pH 依赖性的几个悬而未决的问题，为应用到更复杂的问题奠定了基础，例如铜与神经退行性疾病中涉及的蛋白质的结合。